\section{\-File \-List}
\-Here is a list of all documented files with brief descriptions\-:\begin{DoxyCompactList}
\item\contentsline{section}{include/\hyperlink{algorithm_8hpp}{algorithm.\-hpp} \\*\-N\-M\-Q\-J algorithm for one times tep }{\pageref{algorithm_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{channels_8hpp}{channels.\-hpp} \\*\-Class for representing jump channels. \-Keys form a sequence }{\pageref{channels_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{dtcl4_8hpp}{dtcl4.\-hpp} \\*4th order time convolutionless approximation for decay rate }{\pageref{dtcl4_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{effective__ensemble_8hpp}{effective\-\_\-ensemble.\-hpp} \\*\-Effective ensemble of \-N\-M\-Q\-J method for a single time instant. \-Contains the relevant states for the system dynamics and their probabilities and defines some associated methods }{\pageref{effective__ensemble_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{hamilton_8hpp}{hamilton.\-hpp} \\*\-Class for \hyperlink{classHamiltonian}{\-Hamiltonian} }{\pageref{hamilton_8hpp}}{}
\item\contentsline{section}{include/{\bfseries hamiltonian.\-hpp} }{\pageref{hamiltonian_8hpp}}{}
\item\contentsline{section}{include/{\bfseries input.\-hpp} }{\pageref{input_8hpp}}{}
\item\contentsline{section}{include/{\bfseries jumppaths.\-hpp} }{\pageref{jumppaths_8hpp}}{}
\item\contentsline{section}{include/{\bfseries output.\-hpp} }{\pageref{output_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{random_8hpp}{random.\-hpp} \\*\-Random numbers class }{\pageref{random_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{rate_8hpp}{rate.\-hpp} \\*\-Class for storing decay rates. \-It uses interpolation functions from gsl package }{\pageref{rate_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{simulation_8hpp}{simulation.\-hpp} \\*\-Class for running a simulation }{\pageref{simulation_8hpp}}{}
\item\contentsline{section}{include/\hyperlink{system_8hpp}{system.\-hpp} \\*\-Class for the system definitions }{\pageref{system_8hpp}}{}
\item\contentsline{section}{include/{\bfseries tinystr.\-h} }{\pageref{tinystr_8h}}{}
\item\contentsline{section}{include/{\bfseries tinyxml.\-h} }{\pageref{tinyxml_8h}}{}
\item\contentsline{section}{include/\hyperlink{transition__map_8hpp}{transition\-\_\-map.\-hpp} \\*\-Transition map class }{\pageref{transition__map_8hpp}}{}
\end{DoxyCompactList}
